Job ID = 10451000 sra ファイルのダウンロード中... Completed: 431469K bytes transferred in 13 seconds (260080K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 22696988 spots for /home/okishinya/chipatlas/results/dm3/SRX3404048/SRR6303525.sra Written 22696988 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:14 22696988 reads; of these: 22696988 (100.00%) were unpaired; of these: 656176 (2.89%) aligned 0 times 16050945 (70.72%) aligned exactly 1 time 5989867 (26.39%) aligned >1 times 97.11% overall alignment rate Time searching: 00:18:15 Overall time: 00:18:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1590870 / 22040812 = 0.0722 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Wed, 07 Feb 2018 14:59:00: # Command line: callpeak -t SRX3404048.bam -f BAM -g dm -n SRX3404048.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404048.20 # format = BAM # ChIP-seq file = ['SRX3404048.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 07 Feb 2018 14:59:00: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:59:00: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:59:00: # Command line: callpeak -t SRX3404048.bam -f BAM -g dm -n SRX3404048.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404048.10 # format = BAM # ChIP-seq file = ['SRX3404048.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 07 Feb 2018 14:59:00: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:59:00: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:59:00: # Command line: callpeak -t SRX3404048.bam -f BAM -g dm -n SRX3404048.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404048.05 # format = BAM # ChIP-seq file = ['SRX3404048.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 07 Feb 2018 14:59:00: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:59:00: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:59:13: 1000000 INFO @ Wed, 07 Feb 2018 14:59:14: 1000000 INFO @ Wed, 07 Feb 2018 14:59:20: 1000000 INFO @ Wed, 07 Feb 2018 14:59:27: 2000000 INFO @ Wed, 07 Feb 2018 14:59:31: 2000000 INFO @ Wed, 07 Feb 2018 14:59:39: 3000000 INFO @ Wed, 07 Feb 2018 14:59:41: 2000000 INFO @ Wed, 07 Feb 2018 14:59:48: 3000000 INFO @ Wed, 07 Feb 2018 14:59:51: 4000000 INFO @ Wed, 07 Feb 2018 15:00:02: 3000000 INFO @ Wed, 07 Feb 2018 15:00:03: 5000000 INFO @ Wed, 07 Feb 2018 15:00:06: 4000000 INFO @ Wed, 07 Feb 2018 15:00:13: 6000000 INFO @ Wed, 07 Feb 2018 15:00:17: 4000000 INFO @ Wed, 07 Feb 2018 15:00:22: 7000000 INFO @ Wed, 07 Feb 2018 15:00:23: 5000000 INFO @ Wed, 07 Feb 2018 15:00:27: 5000000 INFO @ Wed, 07 Feb 2018 15:00:31: 8000000 INFO @ Wed, 07 Feb 2018 15:00:37: 6000000 INFO @ Wed, 07 Feb 2018 15:00:40: 9000000 INFO @ Wed, 07 Feb 2018 15:00:42: 6000000 INFO @ Wed, 07 Feb 2018 15:00:47: 7000000 INFO @ Wed, 07 Feb 2018 15:00:48: 10000000 INFO @ Wed, 07 Feb 2018 15:00:57: 11000000 INFO @ Wed, 07 Feb 2018 15:00:58: 8000000 INFO @ Wed, 07 Feb 2018 15:01:02: 7000000 INFO @ Wed, 07 Feb 2018 15:01:06: 12000000 INFO @ Wed, 07 Feb 2018 15:01:10: 9000000 INFO @ Wed, 07 Feb 2018 15:01:16: 13000000 INFO @ Wed, 07 Feb 2018 15:01:20: 8000000 INFO @ Wed, 07 Feb 2018 15:01:21: 10000000 INFO @ Wed, 07 Feb 2018 15:01:29: 14000000 INFO @ Wed, 07 Feb 2018 15:01:30: 11000000 INFO @ Wed, 07 Feb 2018 15:01:35: 9000000 INFO @ Wed, 07 Feb 2018 15:01:47: 12000000 INFO @ Wed, 07 Feb 2018 15:01:49: 15000000 INFO @ Wed, 07 Feb 2018 15:01:56: 10000000 INFO @ Wed, 07 Feb 2018 15:02:04: 13000000 INFO @ Wed, 07 Feb 2018 15:02:09: 16000000 INFO @ Wed, 07 Feb 2018 15:02:14: 11000000 INFO @ Wed, 07 Feb 2018 15:02:15: 14000000 INFO @ Wed, 07 Feb 2018 15:02:26: 15000000 INFO @ Wed, 07 Feb 2018 15:02:28: 17000000 INFO @ Wed, 07 Feb 2018 15:02:31: 12000000 INFO @ Wed, 07 Feb 2018 15:02:37: 16000000 INFO @ Wed, 07 Feb 2018 15:02:41: 18000000 INFO @ Wed, 07 Feb 2018 15:02:48: 17000000 INFO @ Wed, 07 Feb 2018 15:02:49: 13000000 INFO @ Wed, 07 Feb 2018 15:02:58: 18000000 INFO @ Wed, 07 Feb 2018 15:02:59: 19000000 INFO @ Wed, 07 Feb 2018 15:03:06: 14000000 INFO @ Wed, 07 Feb 2018 15:03:09: 19000000 INFO @ Wed, 07 Feb 2018 15:03:17: 20000000 INFO @ Wed, 07 Feb 2018 15:03:19: 20000000 INFO @ Wed, 07 Feb 2018 15:03:22: 15000000 INFO @ Wed, 07 Feb 2018 15:03:24: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:03:24: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:03:24: #1 total tags in treatment: 20449942 INFO @ Wed, 07 Feb 2018 15:03:24: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:03:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:03:24: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:03:24: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:03:24: #1 total tags in treatment: 20449942 INFO @ Wed, 07 Feb 2018 15:03:24: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:03:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:03:24: #1 tags after filtering in treatment: 20449942 INFO @ Wed, 07 Feb 2018 15:03:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:03:24: #1 finished! INFO @ Wed, 07 Feb 2018 15:03:24: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:03:25: #1 tags after filtering in treatment: 20449942 INFO @ Wed, 07 Feb 2018 15:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:03:25: #1 finished! INFO @ Wed, 07 Feb 2018 15:03:25: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:03:26: #2 number of paired peaks: 196 WARNING @ Wed, 07 Feb 2018 15:03:26: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 07 Feb 2018 15:03:26: start model_add_line... INFO @ Wed, 07 Feb 2018 15:03:26: start X-correlation... INFO @ Wed, 07 Feb 2018 15:03:26: end of X-cor INFO @ Wed, 07 Feb 2018 15:03:26: #2 finished! INFO @ Wed, 07 Feb 2018 15:03:26: #2 predicted fragment length is 45 bps INFO @ Wed, 07 Feb 2018 15:03:26: #2 alternative fragment length(s) may be 2,45 bps INFO @ Wed, 07 Feb 2018 15:03:26: #2.2 Generate R script for model : SRX3404048.10_model.r WARNING @ Wed, 07 Feb 2018 15:03:26: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:03:26: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Wed, 07 Feb 2018 15:03:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:03:26: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:03:26: #2 number of paired peaks: 196 WARNING @ Wed, 07 Feb 2018 15:03:26: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 07 Feb 2018 15:03:26: start model_add_line... INFO @ Wed, 07 Feb 2018 15:03:27: start X-correlation... INFO @ Wed, 07 Feb 2018 15:03:27: end of X-cor INFO @ Wed, 07 Feb 2018 15:03:27: #2 finished! INFO @ Wed, 07 Feb 2018 15:03:27: #2 predicted fragment length is 45 bps INFO @ Wed, 07 Feb 2018 15:03:27: #2 alternative fragment length(s) may be 2,45 bps INFO @ Wed, 07 Feb 2018 15:03:27: #2.2 Generate R script for model : SRX3404048.20_model.r WARNING @ Wed, 07 Feb 2018 15:03:27: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:03:27: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Wed, 07 Feb 2018 15:03:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:03:27: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:03:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:03:39: 16000000 INFO @ Wed, 07 Feb 2018 15:03:55: 17000000 INFO @ Wed, 07 Feb 2018 15:04:13: 18000000 INFO @ Wed, 07 Feb 2018 15:04:14: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:04:17: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:04:33: 19000000 INFO @ Wed, 07 Feb 2018 15:04:41: #4 Write output xls file... SRX3404048.10_peaks.xls INFO @ Wed, 07 Feb 2018 15:04:41: #4 Write peak in narrowPeak format file... SRX3404048.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:04:41: #4 Write summits bed file... SRX3404048.10_summits.bed INFO @ Wed, 07 Feb 2018 15:04:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1371 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:04:45: #4 Write output xls file... SRX3404048.20_peaks.xls INFO @ Wed, 07 Feb 2018 15:04:45: #4 Write peak in narrowPeak format file... SRX3404048.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:04:45: #4 Write summits bed file... SRX3404048.20_summits.bed INFO @ Wed, 07 Feb 2018 15:04:45: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:04:52: 20000000 INFO @ Wed, 07 Feb 2018 15:05:00: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:05:00: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:05:00: #1 total tags in treatment: 20449942 INFO @ Wed, 07 Feb 2018 15:05:00: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:05:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:05:00: #1 tags after filtering in treatment: 20449942 INFO @ Wed, 07 Feb 2018 15:05:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:05:00: #1 finished! INFO @ Wed, 07 Feb 2018 15:05:00: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:05:02: #2 number of paired peaks: 196 WARNING @ Wed, 07 Feb 2018 15:05:02: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 07 Feb 2018 15:05:02: start model_add_line... INFO @ Wed, 07 Feb 2018 15:05:02: start X-correlation... INFO @ Wed, 07 Feb 2018 15:05:02: end of X-cor INFO @ Wed, 07 Feb 2018 15:05:02: #2 finished! INFO @ Wed, 07 Feb 2018 15:05:02: #2 predicted fragment length is 45 bps INFO @ Wed, 07 Feb 2018 15:05:02: #2 alternative fragment length(s) may be 2,45 bps INFO @ Wed, 07 Feb 2018 15:05:02: #2.2 Generate R script for model : SRX3404048.05_model.r WARNING @ Wed, 07 Feb 2018 15:05:02: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:05:02: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Wed, 07 Feb 2018 15:05:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:05:02: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:05:52: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:06:22: #4 Write output xls file... SRX3404048.05_peaks.xls INFO @ Wed, 07 Feb 2018 15:06:22: #4 Write peak in narrowPeak format file... SRX3404048.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:06:22: #4 Write summits bed file... SRX3404048.05_summits.bed INFO @ Wed, 07 Feb 2018 15:06:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2374 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。